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InTheLoop | 08.15.2011

August 15, 2011

ESnet Launches Portal with Easy Access to Network Data

ESnet collects a huge amount of data as part of operating and monitoring the network. That data is processed and aggregated in various ways to distill useful information. On August 10, ESnet launched the MyESnet portal, which provides a cohesive view of that information organized through a single unified interface. Read more.

Extreme Computing to Power Energy Science Breakthroughs

Energy science is a broad field that encompasses a diverse group of scientists. But these researchers have a common end in mind: improving energy efficiency, conversion, and storage. In the ASCR Discovery article “Extreme computing to power energy science breakthroughs,” NERSC users Giulia Galli of UC Davis, Ram Devanathan of PNNL, and Jeff Grossman of MIT discuss how their research is contributing to those goals, and how new computational tools will be crucial to further progress.

NSF’s XSEDE to Broadcast DOE ACTS Collection Workshop Tutorials

The Workshop on the DOE Advanced Computational Software (ACTS) Collection, “Scalable and Robust Computational Tools for High-End Computing,” will be held at Sutardja Dai Hall on the UC Berkeley campus Tuesday through Friday this week, August 16–19. This is the twelfth workshop in a series organized by Tony Drummond and Osni Marques of CRD. For the first time this year, the NSF-funded XSEDE partnership (successor to the TeraGrid) will broadcast the ACTS Workshop tutorials to member HPC sites.

The workshop will include a range of tutorials on the tools currently available in the collection, discussion sessions aimed to solve specific computational needs by the workshop participants, and hands-on practice using supercomputers at NERSC. On-site attendance this year is full, so there will be no walk-ins, but webcasts can be viewed here. PDF files from the workshop will be available in the ACTS website.

This year there are 45 attendees—graduate students, postdoctoral fellows, faculty, and research scientists from academia and industry—as well as 17 speakers, mostly from DOE national laboratories. Presentations and hands-on sessions led by CS staff include an introduction to the ACTS Collection by Tony Drummond, ScaLAPACK by Osni Marques, VisIt by Hank Childs, and SuperLU by Sherry Li.

Over the years, more than 500 computational scientists have participated in the ACTS Workshops, teaching them how to fast-track the development of efficient, high-performance applications. Workshop participants also have an opportunity to engage with tool developers and eventually add functionality to the tools.

Vern Paxson, who holds joint appointments at UC Berkeley, the International Computer Science Institute, and Berkeley Lab’s Computational Research Division, has been named recipient of this year’s ACM SIGCOMM Award “for his seminal contributions to the fields of Internet measurement and Internet security, and for distinguished leadership and service to the Internet community.” Read more.

“High performance computing workloads typically pose many challenges to virtualized environments because they stress the memory system and network resources beyond the limits of commercial workloads,” they wrote. To address these problems, the researchers experimentally characterized the main causes of performance degradation of virtualization technologies on non-uniform memory access (NUMA) systems. They showed how to significantly improve the performance on these environments using a specialized runtime mechanism that facilitates the adherence to memory locality.

Last week Associate Lab Director Kathy Yelick was interviewed for Intel’s online Parallel Computing Talk series to discuss the 1.3 petaflop Hopper system at NERSC and to share insights about the programming challenges inherent to petascale and future exascale systems. Her interview starts about 8 minutes into the video. Watch the video. A brief summary of the interview was published in HPCwire.

Book on Science of Music Cites Keith Jackson’s Work with Mickey Hart

A few years ago, CRD computer scientist Keith Jackson, who is also a musician, contributed to “Rhythms of the Universe,” a musical project to “sonify” the universe by Grateful Dead percussionist Mickey Hart, that was performed at the Cosmology at the Beach Conference held January 11-15, 2010 in Playa del Carmen, Mexico, sponsored by George Smoot’s Berkeley Center for Cosmological Physics. Jackson converted the electromagnetic data from exploding supernova light waves by slowing down the frequency and elongating or “stretching” it into audio form; Hart then took the sounds and incorporated them into his musical composition. (Read the 2010 CS news feature.)

That collaboration has been cited in the recent book The Power of Music: Pioneering Discoveries in the New Science of Song by Elena Mannes.(Read the excerpt.) According to Mannes, we are at a breakthrough moment in music research, for only recently has science sought in earnest to understand and explain the power of music and its connection to the body, the brain, and the world of nature. Music may even contain organizing principles of harmonic vibration that underlie the cosmos itself, as exemplified in Jackson and Hart’s supernova music.

Mannes has won six Emmys for her documentaries and is a member of one of the first families of American music. Her grandparents founded the Mannes College of Music in New York City; and her great uncle, Walter Damrosch, conducted the Metropolitan Opera and was the instigator for the building of Carnegie Hall.

Safety Suggestions Are Due August 31

As part of Berkeley Lab’s initiative to transform our safety culture, Computing Sciences sponsors an ongoing CS Top 10 Safety Competition. Submittals for our current round of safety suggestions are due August 31. Employees who submit the winning entries will be recognized with Spot Awards.

To participate, send near-miss safety hazards and safety suggestions to Safety Coordinator Betsy MacGowan at 510-495-2826. Read more about the program and see past winners here.

This Week’s Computing Sciences Seminars

The quest for building an exascale system at the end of this decade has brought the key challenges to the forefront — energy efficient, fault tolerant (and scalable) programming models. In this talk, I will present ongoing research on energy efficient algorithms, programming models and communication runtime systems and study the characteristics with modern architectures. I will also talk about fault tolerant PGAS data store models with task-based execution models addressing multiple classes of faults. Performance results using NWChem, STOMP, Sweep3D with Global Arrays, MPI and ARMCI on interconnects such as Gemini, Seastar2, and InfiniBand will be presented.

NERSC security routinely blocks network traffic from external hosts that appear to be hostile. Up to now, the mechanism we’ve used to do this has been an access control list (ACL) configured into our core router. While this method has served us well for many years, we are reaching the limits of its effectiveness. To address this, we’re changing to a different mechanism for blocking, known as remotely triggered black hole (RTBH) filtering. In this talk I will describe both methods of blocking. I’ll present the results of testing that show the new method to be a significant improvement over the old method. And I’ll discuss why RTBH filtering performs so much better than an ACL in a router.

Link of the Week: Bubbly Eternal Inflation, or: Next Step Infinity The question of whether the world is finite or infinite has bedeviled us for a long time. It was a classic question in ancient Indian philosophy. Aristotle cogently argued that while infinity made sense in the “potential,” the world could not “actually” be infinite. Giordano Bruno declared the world infinite and was burned at the stake. Galileo, more circumspect, had his clever alter ego, Salviati, completely befuddle Simplicio with how paradoxical and slippery infinity is. And Immanuel Kant really threw down the gauntlet, arguing that both an infinite and a finite world were logically impossible. It might appear that the question could most conveniently be consigned to the dust heap of purely philosophical inquiries that hard-nosed scientists can safely ignore.

Yet Albert Einstein’s theories of space and time radically reformulated the questions of finite and infinite spaces and times, and the ensuing development of cosmology has brought infinity into the domain of testable physical science. For example, a uniform space can be curved like a sphere—and comprise a universe that is finite in volume without having any “edge” or empty space outside it. Even more impressive are the tricks that relativity can play concerning infinite spaces, which have come to occupy a central place in contemporary cosmology.

Anthony Aguirre, an associate professor of physics at the University of California, Santa Cruz, contends that:

It is logically possible for a finite spatial region to evolve into a space that is both uniform and spatially infinite.

Inflation, our well-tested and widely accepted paradigm for understanding the very early universe, provides just the right physics and context for this to happen.

In the combination of our current best bets for cosmology and fundamental physics, inflation creates infinitely many “subuniverses,” each itself uniform and infinite.

This raises profound issues—for physics, cosmology, and even personal identity—that we cannot ignore.

The Lawrence Berkeley National Laboratory (Berkeley Lab) Computing Sciences organization provides the computing and networking resources and expertise critical to advancing the Department of Energy's research missions: developing new energy sources, improving energy efficiency, developing new materials and increasing our understanding of ourselves, our world and our universe.

ESnet, the Energy Sciences Network, provides the high-bandwidth, reliable connections that link scientists at 40 DOE research sites to each other and to experimental facilities and supercomputing centers around the country. The National Energy Research Scientific Computing Center (NERSC) powers the discoveries of 6,000 scientists at national laboratories and universities, including those at Berkeley Lab's Computational Research Division (CRD). CRD conducts research and development in mathematical modeling and simulation, algorithm design, data storage, management and analysis, computer system architecture and high-performance software implementation. NERSC and ESnet are DOE Office of Science User Facilities.

Lawrence Berkeley National Laboratory addresses the world's most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab's scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the DOE’s Office of Science.

DOE’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.